• Proceedings of the KAIS Fall Conference
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• 2010.05b
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• pp.1201-1204
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• 2010

최근, 마이크로어레이 실험 데이터의 품질과 재 생산성에 대한 신뢰도가 증가했기 때문에 마이크로어레이 데이터의 공유 및 활용에 대한 요구가 꾸준히 증가하고 있다. 하지만, 개별적으로 진행되는 이 실험에서, 연구자는 각각의 실험계획에 따른 실험을 위해 별도로 실험계획을 하고, 그에 따른 단편적인 결과를 얻을 뿐, 이를 다시 재활용 하는 방안에는 microarray databases를 이용하는 것만이 전부였다. 하지만, 이 방법은 일반 생물학자들이, 다시 데이터베이스를 이용해서 분석하는데 많은 어려움을 가져왔고, 또한 각각의 실험 과정을 이용하는 과정에서도, 통합개발환경을 구축하지 못 한 것에 대해 시간적 손해를 많이 입고 있다. 이에 본 논문에서는 실험계획부터 자료의 표준화 및 시각화, 유의한 유전자 탐색, 군집분석, 분류분석을 할 수 있는 통합개발환경 프로그램에 대해 제시하고, 결론적으로 이 데이터를 효과적으로 재활용 할 수 있는 방안에 대해서 제시하였다. 결론적으로, 이 프로그램은 개별적인 통계 프로그램으로 분석을 할 때에 비해, 편의성이 향상하며, 시간적인 소모를 줄임으로써, 상당히 많은 이득을 얻을 수 있으며, 한번 분석한 데이터를 효율적으로 저장해 놓음으로써, 추후에 제 2,3의 데이터 가공을 통해, 더 많은 정보를 얻어 낼 수 있다.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.4 no.4
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• pp.739-744
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• 2000

As DNA sequences have been known through the Genome project the techniques for dealing with molecule-level gene information are being made researches briskly. It is also urgent to develop new computer algorithms for making databases and analyzing it efficiently considering the vastness of the information for known sequences. In this respect, this paper studies the association rule search algorithms for finding out the characteristics shown by means of the association between promoter sequences and genes, which is one of the important research areas in molecular biology. This paper treat biological data, while previous search algorithms used transaction data. So, we design a transformed association rule algorithm that covers data types and biological properties. These research results will contribute to reducing the time and the cost for biological experiments by minimizing their candidates.

• Journal of Plant Biotechnology
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• v.42 no.3
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• pp.245-256
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• 2015

In the agricultural industries, LEDs are used as supplementary, as well as main lighting sources in closed cultivation systems. In cultivation using artificial light sources, various light qualities have been tried to supplement fluorescent lamps to promote plant growth and metabolism. Microarray analysis of Brassica rapa seedlings under blue and fluorescent mixed with blue light conditions identified changes in three genes of the glucosinolate pathway. This attracted attention as functional materials highly expressed 3.6-4.6 fold under latter condition. We selected four more genes of the glucosinolate pathway from the Brassica database and tested their expression changes under fluorescent light mixed with red, green, and blue, respectively. Some genes increased expression under red and blue mixed conditions. The Bra026058, Bra015379, and Bra021429; the orthologous genes of CYP79F1, ST5a, and FMOGS-OX1 in Arabidopsis, are highly expressed in Brassica rapa under fluorescent mixed with blue light conditions. Further, Bra029355, Bra034180, Bra024634, and Bra022448; the orthologous genes of MAM1, AOP3, UGT74B1, and BCAT4 in Arabidopsis, are highly expressed in Brassica rapa under fluorescent mixed with red light conditions. The various light conditions had unique effects on the varieties of Brassica, resulting in differences in glucosinolate synthesis. However, in some varieties, glucosinolate synthesis increased under mixed blue light conditions. These results will help to construct artificial light facilities, which increase functional crops production.

• Journal of Life Science
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• v.19 no.4
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• pp.449-456
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• 2009

Murine Neuro-2a (N2a) cells have been widely used for the investigation of neuronal differentiation, trophic interaction and neurotoxic effects of various compounds and their associated mechanisms. N2a cells have many genomic variations such as gains or losses in DNA copy number, similar to other neuroblastoma cells, and no systematic or high-resolution studies of their genome-wide chromosomal aberrations have been reported. Presently, we conducted a systematic genome-wide determination of chromosomal aberrations in N2a cells using a high-throughput, oligonucleotide array-based comparative genomic hybridization (oaCGH) technique. A hidden Markov Model was employed to assign each genomic oligonucleotide to a DNA copy number state: double loss, single loss, normal, gain, double gain and amplification. Unlike most neuroblastoma cells, Mycn amplification was not observed in N2a cells. In addition, these cells showed gain only in the neuron-derived neurotrophic factor (NF), while other neurotrophic factors such as glial line-derived NF and brain-derived NF presented normal copy numbers. Chromosomes 4, 8, 10, 11 and 15 displayed more than 1000 aberrational oligonucleotides, while chromosomes 3, 17, 18 and 19 displayed less than 20. The largest region of gain was located on chromosome 8 and its size was no less than 26.7 Mb (Chr8:8427841-35162415), while chromosome 4 had the longest region of single deletion, with a size of 15.1 Mb (Chr4:73265785-88374165).

• Journal of KIISE:Software and Applications
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• v.31 no.9
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• pp.1233-1245
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• 2004

Though biometrics to authenticate a person is a good tool in terms of security and convenience, typical authentication algorithms using biometrics may not be executed on resource-constrained devices such as smart cards. Thus, to execute biometric processing on resource-constrained devices, it is desirable to develop lightweight authentication algorithm that requires only small amount of memory and computation. Also, among biological features, face is one of the most acceptable biometrics, because humans use it in their visual interactions and acquiring face images is non-intrusive. We present a new face authentication algorithm in this paper. Our achievement is two-fold. One is to present a face authentication algorithm with low memory requirement, which uses support vector machines (SVM) with the feature set extracted by genetic algorithms (GA). The other contribution is to suggest a method to reduce further, if needed, the amount of memory required in the authentication at the expense of verification rate by changing a controllable system parameter for a feature set size. Given a pre-defined amount of memory, this capability is quite effective to mount our algorithm on memory-constrained devices. The experimental results on various databases show that our face authentication algorithm with SVM whose input vectors consist of discriminating features extracted by GA has much better performance than the algorithm without feature selection process by GA has, in terms of accuracy and memory requirement. Experiment also shows that the number of the feature ttl be selected is controllable by a system parameter.

• Microbiology and Biotechnology Letters
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• v.31 no.3
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• pp.216-223
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• 2003

A 1.3-kb of chitosanase gene (choA) encoding 45-kDa polypeptide was cloned, expressed, and characterized from a newly isolated Bacillus cereus H-1. The chitosanase protein (ChoA) of B. cereus H-l was purified to homogeneity by ammonium sulfate precipitation and CM-sephadex column chromatography. Optimum pH was around 7, and stable pH range in the incubation at 50 C was 4-11. Optimum temperature was around 50 C, and enzyme activity was relatively stable below 45 C. ChoA showed the activities toward carboxymethyl cellulose (CMC) in addition to soluble or glycol chitosan. Based on MALDI-TOF MS analysis of purified ChoA, the entire amino acid sequence of ChoA was interpreted by database searching of previously known Bacillus chitosanases. A 1.6 kb of PCR product of corresponding chitosanase gene was obtained and its DNA sequence was determined. The deduced amino acid of choA revealed that ChoA have a 98% homology with those of Bacillus sp. No.7-M strain and Bacillus sp. KCTC0377BP. The recombinant ChoA protein was expressed in E. coli DH5$\alpha$. Deduced amino acid comparison of choA with other chitosanases suggested that it belongs to family 8 microbial endo-chitosanase with chitosanase-cellulase activity.

• Journal of the Korean Society of Food Science and Nutrition
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• v.45 no.6
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• pp.911-917
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• 2016

Lespedeza cuneata G. Don is an edible perennial herb used in traditional Korean medicine. We investigated the anti-proliferative properties and mechanism of L. cuneata extract. The ethanolic extract of L. cuneata dose-and time-dependently inhibited human colorectal cancer cell proliferation. A 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) assay was used to test the effect of the extract on proliferation of HT-29 colorectal cancer cells. The extract inhibited HT-29 cell proliferation with an $IC_{50}$ value of $554.26{\pm}8.81{\mu}g/mL$. L. cuneata extract suppressed production of pro-inflammatory cytokines interleukin-6 and tumor necrosis $factor-{\alpha}$. Apoptosis was evaluated by analysis of DNA fragmentation, poly(ADP-ribose) polymerase cleavage, caspase-3 activity, and protein expression of pro-apoptotic (Bax) and anti-apoptotic (Bcl-2). Our results demonstrated that the extract induced DNA fragmentation and characteristic morphological changes associated with apoptosis in HT-29 colorectal cancer cells. The extract also time- and dose-dependently up-regulated expression of the Bax and down-regulated expression of the Bcl-2. Furthermore, the extract dose- and time-dependently enhanced caspase-3 activity. Our findings provide evidence that L. cuneata extract may mediate its anti-proliferative effect via modulation of apoptosis.

• The Korean Journal of Malacology
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• v.20 no.2
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• pp.165-169
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• 2004

The BLAST server for the mollusk was constructed on the basis of the Intel Server Platform SC-5250 dual Xeon 2.8 GHz cpu and Linux operating system. After establishing the operating system, we installed NCBI (National Center for Biotechnology Information) WebBLAST package after web server configuration for cgi (common gate interface) (http://chimp.kribb.re.kr/mollusks). To build up the stand alone blast, we conducted as follows: First, we downloaded the genome information (mitochondria genome information), DNA sequences, amino acid sequences related with mollusk available at NCBI. Second, it was translated into the multifasta format that was stored as database by using the formatdb program provided by NCBI. Finally, the cgi was used for the Stand Alone Blast server. In addition, we have added the vector, Escherichia coli, and repeat sequences into the server to confirm a potential contamination. Finally, primer3 program is also installed for the users to design the primer. The stand alone BLAST gave us several advantages: (1) we can get only the data that agree with the nucleotide sequence directly related with the mollusks when we are searching BLAST; (2) it will be very convenient to confirm contamination when we made the cDNA or genomic library from mollusks; (3) Compared to the current NSBI, we can quickly get the BLAST results on the mollusks sequence information.

• Journal of Life Science
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• v.24 no.9
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• pp.995-1000
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• 2014

The studies of marine viruses in terms of viral isolation and detection have been limited due to the high mutation rate and genetic diversity of marine viruses. Of the modern methods currently used to detect marine viruses, serological methods based on enzyme-linked immunosorbent assay (ELISA) are the most common. They depend largely on the quality of the antibodies and on highly purified suitable antigens. Recently, a new experimental system for using viral capsid protein as an antigen has been developed using the yeast surface display (YSD) technique. In the present study, the capsid protein gene of the red-spotted grouper nervous necrosis virus (RGNNV) was expressed and purified via YSD and HA-tagging systems, respectively. Two regions of the RGNNV capsid protein gene, RGNNV1 and RGNNV2, were individually synthesized and subcloned into a yeast expression vector, pCTCON. The expressions of each RGNNV capsid protein in the Saccharomyces cerevisiae strain EBY100 were indirectly detected by flow cytometry with fluorescently labeled antibodies, while recognizing the C-terminal c-myc tags encoded by the display vector. The expressed RGNNV capsid proteins were isolated from the yeast surface through the cleavage of the disulfide bond between the Aga1 and Aga2 proteins after ${\beta}$-mercaptoethanol treatment, and they were directly detected by Western blot using anti-HA antibody. These results indicated that YSD and HA-tagging systems could be applicable to the expressions and purification of recombinant RGNNV capsid proteins.

• Journal of Life Science
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• v.30 no.12
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• pp.1063-1069
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• 2020

Two crucian carp species (Carassius auratus and C. cuvieri) inhabit Lake Yedang in South Korea, and C. auratus is known to be native to Korea. Classification of these two freshwater fish species is often confused because of their morphological similarity. To distinguish the two species, we conducted phylogenetic and population genetic analyses of C. auratus and C. cuvieri based on their mitochondrial DNA sequences of the cytochrome b gene (CYTB). We also compared our partial CYTB sequence (<1,056 bp) with 10 Chinese, nine Japanese, and two Russian crucian carp fishes. The results of our phylogenetic analysis showed that C. auratus and C. cuvieri were clearly divided into two phylogroups. The nucleotide diversity (π) of C. auratus from Korea, China, and Japan showed a range of 0.146%~0.421%, while the range of π of C. cuvieri from Korea and Japan was lower than those of C. auratus (0.0%~0.054%). Moreover, the comparison of CYTB divergence among crucian carp fishes in China, Japan, and Korea indicated that Korean Carassius fishes were distantly related to those from China and Japan, with two exceptions: the pairwise Fst value between Korean C. auratus and northern Chinese C. auratus was not significantly different. In addition, no significant genetic divergence between Korean and Japanese C. cuvieri was detected. We conclude that, despite the morphological similarities, C. auratus and C. cuvieri should be considered as separate freshwater fish resources in conservation efforts for genetic diversity.